Table 2.

Summary of parameter estimates and likelihood scores for the model of best fit showing evidence of positive selection

Gene	Model	lnL	Parameter Estimates	Positive Selection	BEB Positively Selected Sites
Lineage-Specific Analyses
Euarchontoglires Ancestral Branch
STK11	modelA	−8602.921472	p0 = 0.93299, p1 = 0.05633, p2 = 0.01007, p3 = 0.00061 ω0 = 0.03346, ω1 = 1.00000, ω2 = 197.90897	Yes	3 > 0.50, 1 > 0.95, 0 > 0.99
Primate Ancestral Branch
CDH1	modelA	−16658.03484	p0 = 0.75454, p1 = 0.23453, p2 = 0.00834, p3 = 0.00259 ω0 = 0.05683, ω1 = 1.00000, ω2 = 10.20516	Yes	9 > 0.50, 1 > 0.95, 0 > 0.99
Hominidae Ancestral Branch
STK11	modelA	−8601.056009	p0 = 0.93574, p1 = 0.05920, p2 = 0.00476, p3 = 0.00030 ω0 = 0.03323, ω1 = 1.00000, ω2 = 44.31709	Yes	3 > 0.50, 2 > 0.95, 1 > 0.99
VHL	modelA	−4263.853291	p0 = 0.73748, p1 = 0.25109, p2 = 0.00853, p3 = 0.00290 ω0 = 0.05985, ω1 = 1.00000, ω2 = 220.34533	Yes	1 > 0.50, 0 > 0.95, 0 > 0.99
Chimpanzee Extant Branch
TSC2	modelA	−42659.27711	p0 = 0.90352, p1 = 0.09434, p2 = 0.00194, p3 = 0.00020 ω0 = 0.04404, ω1 = 1.00000, ω2 = 190.09480	Yes	6 > 0.50, 2 > 0.95, 2 > 0.99
VHL	modelA	−4262.098043	p0 = 0.73571, p1 = 0.25251, p2 = 0.00877, p3 = 0.00301 ω0 = 0.05976, ω1 = 1.00000, ω2 = 262.72662	Yes	3 > 0.50, 0 > 0.95, 0 > 0.99
Gorilla Extant Branch
MSH2	modelA	−19485.4338	p0 = 0.92233, p1 = 0.06298, p2 = 0.01375, p3 = 0.00094 ω0 = 0.06427, ω1 = 1.00000, ω2 = 999.00000	Yes	46 > 0.50, 34 > 0.95, 18 > 0.99
TSC2	modelA	−42569.22884	p0 = 0.89862, p1 = 0.08796, p2 = 0.01222, p3 = 0.00120 ω0 = 0.04339, ω1 = 1.00000, ω2 = 999.00000	Yes	27 > 0.50, 14 > 0.95, 12 > 0.99
MSH6	modelA	−34009.90221	p0 = 0.78382, p1 = 0.18418, p2 = 0.02591, p3 = 0.00609 ω0 = 0.06974, ω1 = 1.00000, ω2 = 999.00000	Yes	46 > 0.50, 34 > 0.95, 18 > 0.99
ATM	modelA	−69374.08393	p0 = 0.80673, p1 = 0.17971, p2 = 0.01109, p3 = 0.00247 ω0 = 0.09745, ω1 = 1.00000, ω2 = 999.00000	Yes	48 > 0.50, 23 > 0.95, 19 > 0.99
Orangutan Extant Branch
TSC1	modelA	−24068.71106	p0 = 0.79963, p1 = 0.18828, p2 = 0.00978, p3 = 0.00230 ω0 = 0.08020, ω1 = 1.00000, ω2 = 999.00000	Yes	13 > 0.50, 6 > 0.95,5 > 0.99
TSC2	modelA	−42673.92339	p0 = 0.90414, p1 = 0.09295, p2 = 0.00263, p3 = 0.00027 ω0 = 0.04433, ω1 = 1.00000, ω2 = 40.47366	Yes	9 > 0.50, 0 > 0.95, 0 > 0.99
Marmoset Extant Branch
TSC2	modelA	−42616.04524	p0 = 0.89841, p1 = 0.09019, p2 = 0.01035, p3 = 0.00104 ω0 = 0.04325, ω1 = 1.00000, ω2 = 235.10448	Yes	38 > 0.50, 9 > 0.95
MSH6	modelA	−34009.90221	p0 = 0.78382, p1 = 0.18418, p2 = 0.02591, p3 = 0.00609 ω0 = 0.06974, ω1 = 1.00000, ω2 = 999.00000	Yes	45 > 0.50, 16 > 0.95, 12 > 0.99
VHL	modelA	−4262.443441	p0 = 0.72045, p1 = 0.22453, p2 = 0.04195, p3 = 0.01307 ω0 = 0.05886, ω1 = 1.00000, ω2 = 90.26952	Yes	10 > 0.50, 0 > 0.95, 0 > 0.99
ATM	modelA	−69583.23068	p0 = 0.81640, p1 = 0.18148, p2 = 0.00173, p3 = 0.00038 ω0 = 0.09939, ω1 = 1.00000, ω2 = 46.82466	Yes	2 > 0.50, 0 > 0.95, 0 > 0.99
Muridae Ancestral Branch
TSC1	modelA	−24126.17894	p0 = 0.80995, p1 = 0.18416, p2 = 0.00481, p3 = 0.00109 ω0 = 0.08293, ω1 = 1.00000, ω2 = 999.00000	Yes	1 > 0.59, 0 > 0.95, 0 > 0.99
Murinae Ancestral Branch
SDHC	modelA	−3846.690164	p0 = 0.87666, p1 = 0.08131, p2 = 0.03846, p3 = 0.00357 ω0 = 0.15340, ω1 = 1.00000, ω2 = 253.61375	Yes	9 > 0.50, 2 > 0.95, 1 > 0.99
MSH6	modelA	−34190.13821	p0 = 0.79911, p1 = 0.19671, p2 = 0.00335, p3 = 0.00082 ω0 = 0.07057, ω1 = 1.00000, ω2 = 126.22513	Yes	3 > 0.50, 1 > 0.95, 0 > 0.99
Rat Extant Branch
MADH4	modelA	−6092.186945	p0 = 0.93360, p1 = 0.01536, p2 = 0.05021, p3 = 0.00083 ω0 = 0.01379, ω1 = 1.00000, ω2 = 102.33013	Yes	24 > 0.50, 11 > 0.95, 10 > 0.99
NF1	modelA	−37750.29866	p0 = 0.96609, p1 = 0.02476, p2 = 0.00892, p3 = 0.00023 ω0 = 0.02265, ω1 = 1.00000, ω2 = 999.00000	Yes	39 > 0.50, 10 > 0.95, 10 > 0.99
Guinea pig Extant Branch
TSC1	modelA	−24116.58577	p0 = 0.80206, p1 = 0.18611, p2 = 0.00961, p3 = 0.00223 ω0 = 0.08093, ω1 = 1.00000, ω2 = 284.22603	Yes	9 > 0.50, 4 > 0.95, 0 > 0.99
NF1	modelA	−37849.50819	p0 = 0.97375, p1 = 0.02506, p2 = 0.00116, p3 = 0.00003 ω0 = 0.02414, ω1 = 1.00000, ω2 = 171.64068	Yes	3 > 0.50, 1 > 0.95, 0 > 0.99
Rabbit Extant Branch
MLH1	modelA	−19516.63525	p0 = 0.80595, p1 = 0.18541, p2 = 0.00703, p3 = 0.00162 ω0 = 0.05262, ω1 = 1.00000, ω2 = 7.52747	Yes	5 > 0.05, 3 > 0.95, 0 > 0.99
MUTYH	modelA	−15911.6175	p0 = 0.61027, p1 = 0.37605, p2 = 0.00846, p3 = 0.00522 ω0 = 0.07703, ω1 = 1.00000, ω2 = 998.99697	Yes	5 > 0.50, 4 > 0.95, 3 > 0.99
SDHC	modelA	−3822.683246	p0 = 0.57771, p1 = 0.06636, p2 = 0.31926, p3 = 0.03667 ω0 = 0.12047, ω1 = 1.00000, ω2 = 3.59059	Yes	51 > 0.50, 10 > 0.95, 8 > 0.99
ATM	modelA	−69582.95152	p0 = 0.81572, p1 = 0.18045, p2 = 0.00313, p3 = 0.00069 ω0 = 0.09930, ω1 = 1.00000, ω2 = 7.41594	Yes	6 > 0.50, 0 > 0.95, 0 > 0.99
BHD	modelA	−13523.51719	p0 = 0.90728, p1 = 0.05930, p2 = 0.03137, p3 = 0.00205 ω0 = 0.02817, ω1 = 1.00000, ω2 = 6.50017	Yes	10 > 0.50, 7 > 0.95, 1 > 0.99
Site-specific Analyses
CDH1	m8	−16589.88768	p = 0.21848, p0 = 0.99291, p1 = 0.00709, q = 0.80842 ω=4.53766	Yes	15 > 0.5, 1 > 0.95, 0 > 0.99
PMS1	m8	−26480.39761	p = 0.61337, p0 = 0.93580, p1 = 0.06420, q = 1.93110 ω=1.32691	Yes	25 > 0.50, 1 > 0.95, 0 > 0.99
PMS2	m8	−27449.3651	p = 0.29104, p0 = 0.91064, p1 = 0.08936, q = 1.31619 ω=1.28855	Yes	37 > 0.50, 1 > 0.95, 0 > 0.99
MUTYH	m8	−15797.6226	p = 0.37255, p0 = 0.97242, p1 = 0.02758, q = 1.00900 ω=2.44412	Yes	18 > 0.5, 1 > 0.95, 0 > 0.99
TP53	m8	−8688.19126	p = 0.40362, p0 = 0.94645, p1 = 0.05355, q = 1.77507 ω=1.97385	Yes	13 > 0.5, 3 > 0.95, 0 > 0.99

The model of best fit is summarized below for those genes with evidence of positive selection. The lineage-specific results for each lineage tested from the Euarchontoglires ancestor to modern lineages are shown in the top panel and the site-specific results are shown in the bottom panel. The model abbreviations are as per main text. P refers to the number of free parameters estimated in that model. BEB = Bayes Empirical Bayes estimations. The number of positively selected sites identified can be found the final column, sites are separated by the posterior probability cutoffs of 0.50, 0.95, and 0.99.